[[TracNav(xQTL)]]

= [wiki:xQTL xQTL workbench] - Browse or search available data =

Start by exploring the data by click on ''Browse data'' in the main menu. This will take you to a screen with four tabs, which are explained in more detail below.

=== Overview ===

* The first tab named ''Overview'' will present you with a summary view of all entries in this investigation.
* You can change investigations with the arrowed buttons at the top.
* Clicking on a type of data will take you there. This is a shorthand: you can always browse to all datatypes using the tabs ''View data'', ''View annotations'', and ''View files''.
* Similarly, the ''Add'' button is a shorthand to be taken to the tabs of this data category (data, annotations or file) where you can start adding data with the ''Add new record'' button.
* The default view will display 4 entries for each type: use ''Show all'' to expand.

=== View data ===

* This tab allows you to add, view and remove data matrices. These are rectangular pieces of (raw) experimental data accompanied by row- and column names.
* Matrices themselves are annoted with the 'Data' entries, while their row- and column entries are annotated as separate (strong) datatypes found in the ''View annotations'' tab.
* There are a number of plugins that will help you deal with matrices:
 * Manager = Uploads data and views the numerical/textual data.
 * Heatmap = View numerical values as a customizable heatmap.
 * Rplot = Create graphical plots using R.
 * Inspector = Check whether annotations are missing.
 * Delete storage = Delete source data linked to this Data entry.

=== View annotations ===

* This section allows you to add, view and remove annotations such as ''Individual'', ''Gene'' or ''Marker''.
* These annotations are often linked to a data matrix, but they don't have to be.
* You can view display a list of records which is manipulatable using the ''View'' menu, search box, or paging buttons.
* When clicking ''edit record'' you can change the values of a record.
* Click ''More annotions'' to see more exotic data types such as ''!DerivedTrait'' or ''!EnvironmentalFactor''.

=== View files ===

* Here you can add files in their original form to the database.
* Specify the name and extension of the file in a standard record. Try making a file named 'test' with extension 'txt'. Save the record.
* You will now see an upload window. Files can be added by selecting them from your filesystem, or by typing in the text area. Try typing 'this is my file', and press the lower-right ''Upload'' button.
* A viewer will serve out the contents based on the extension. A photo (e.g. PNG) will result in a visible picture. Text is rendered as plain (non editable) text.
* Using the ''delete current record'' button will remove the file entry and the associated file.
* Files with extension 'FIG' (an R plot format) will be rendered by a special applet. You might need to install Java in your browser to view it.